Interpretive Summary: Submergence stress can cause the death of ryegrass. Genetic differences in submergence tolerance were observed among ryegrass germplasm lines. Molecular markers associated with submergence tolerance will facilitate selection of tolerant cultivars for commercial production. After 96 ryegrass lines from different origins were subemerged in water for 7 days, their leaf color, chlorophyll fluorescence (Fv/Fm), maximum plant height (HT), and relative growth rate (RGR) were significantly reduced. However, significant variation in these traits was observed among accessions. Marker analysis identified four subpopulations in the collection. Fifteen DNA markers were associated with reduction in green color, Fv/Fm, HT, and RGR. The identified submergence-tolerant germplasm and markers should be useful for genetic improvement of submergence tolerance of perennial ryegrass.

Technical Abstract:
Submergence stress can cause the death of turfgrass plants. Identification of association between molecular markers and submergence tolerance-related traits facilitates an efficient selection of the tolerant cultivars for commercial production. A global collection of 99 diverse perennial ryegrass (Lolium perenne) accessions was evaluated for 109 simple sequence repeat (SSR) markers. Submergence significantly reduced leaf green color, chlorophyll fluorescence (Fv/Fm), maximum plant height (HT), and relative growth rate (RGR). Significant variations in these trait values were observed among the accessions under submerged conditions. Rapid linkage-disequilibrium (LD) decay was observed within 4 cM. The analysis of population structure (Q) identified four subpopulations in the collection, but obvious relative kinship (K) was not found. The Q model was the best to describe association between SSR and traits, compared to the simple linear model, K, and Q + K models. Fifteen SSR markers were associated with a reduction in leaf color, Fv/Fm, HT, and RGR under submergence stress using the Q model. These markers can be used for genetic improvement of submergence tolerance of perennial ryegrass after further validation. The diverse population of perennial ryegrass is a valuable recourse for association mapping of stress tolerance-related physiological traits.